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Releases: SMI/SmiServices

v5.9.0

04 Oct 06:21
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Feature

  • #1945 by rkm. Add a publish timeout backoff mechanism to ProducerModel, allowing control over message publishing timeout behaviour. This can be enabled by setting BackoffProviderType in any ProducerOptions config. Currently implemented types are:

    • StaticBackoffProvider (1 minute flat timeout)
    • ExponentialBackoffProvider (1 minute initial, doubling after each timeout)

  • #1952 by rkm. Enable pausing of message publishing based on monitoring downstream queue message count

Bugfix

  • #1954 by rkm. Fix program names in MessageHeader and logging setup

What's Changed

  • Bump MongoDB.Bson from 2.28.0 to 2.29.0 by @dependabot in #1942
  • Bump com.rabbitmq:amqp-client from 5.21.0 to 5.22.0 in /src/common/com.smi.microservices.parent by @dependabot in #1943
  • Feature/extraction rate limiting by @rkm in #1945
  • Bump HIC.RDMP.Plugin and MongoDB.Driver by @dependabot in #1944
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.17.2 to 2.18.0 in /src/common/com.smi.microservices.parent by @dependabot in #1946
  • Bump org.mockito:mockito-core from 5.13.0 to 5.14.0 in /src/common/com.smi.microservices.parent by @dependabot in #1947
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.17.2 to 2.18.0 in /src/common/com.smi.microservices.parent by @dependabot in #1948
  • Bump YamlDotNet from 16.1.2 to 16.1.3 by @dependabot in #1949
  • Bump HIC.RDMP.Plugin.Test from 8.2.3 to 8.3.0 by @dependabot in #1950
  • Bump actions/setup-java from 4.3.0 to 4.4.0 by @dependabot in #1951
  • Enable pausing of message publishing based on monitoring downstream queue message count by @rkm in #1952
  • Fix program names in MessageHeader and logging setup by @rkm in #1954
  • Release v5.9.0 by @rkm in #1955

Full Changelog: v5.8.0...v5.9.0

Contributors

rkm and dependabot
Assets 7
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v5.8.0

19 Sep 20:47
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v5.8.0

Feature

  • #1938 by rkm. Allow specifying path to DynamicRules file

Bugfix

  • #1892 by rkm. docker-compose replaced by docker compose
  • #1917 by rkm. Fix handling of GlobalOptions deserializing to null
  • #1939 by rkm. Fix loading of TesseractEngine on Linux
  • #1940 by rkm. Bump sqlserver to 2022 in CI to fix startup crash

Change

  • #1879 by jas88. Remove Oracle remnants, fill in some gaps in Postgresql support instead
  • #1894 by rkm. Condense all code into 2 csprojs
  • #1901 by rkm. Switch coverage collection from coverlet.msbuild to Microsoft.CodeCoverage and dotnet-coverage
  • #1902 by rkm. Separate unit and integration tests into separate projects
  • #1903 by rkm. Run automated Visual Studio code cleanup & apply fixes
  • #1906 by jas88. Exclude test code from test coverage calculations since testing tests makes no sense

Meta

  • #1891 by rkm. Tidy & auto-format codebase

What's Changed

  • Less Oracle, more cowb - er, Postgresql by @jas88 in #1879
  • use docker compose over docker-compose by @rkm in #1892
  • Tidy & auto-format by @rkm in #1891
  • Bump HIC.RDMP.Dicom from 7.0.7 to 7.0.8 by @dependabot in #1895
  • Bump org.hamcrest:hamcrest-library from 2.2 to 3.0 in /src/common/com.smi.microservices.parent by @dependabot in #1898
  • Condense csprojs by @rkm in #1894
  • Bump HIC.RDMP.Plugin.Test, HIC.RDMP.Plugin, MongoDB.Driver and MongoDB.Bson by @dependabot in #1900
  • fix coverage reporting by @rkm in #1901
  • Separate unit/integration tests by @rkm in #1902
  • Bump actions/setup-java from 4.2.1 to 4.2.2 by @dependabot in #1905
  • Exclude tests from test coverage to avoid recursive self-coverage by @jas88 in #1906
  • Bump NUnit.Analyzers from 4.2.0 to 4.3.0 by @dependabot in #1904
  • run VS automated code cleanups by @rkm in #1903
  • Bump NLog from 5.3.2 to 5.3.3 by @dependabot in #1907
  • Bump HIC.BadMedicine.Dicom from 0.1.0 to 0.1.1 by @dependabot in #1908
  • Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.10.0 to 4.11.0 by @dependabot in #1909
  • Bump NLog from 5.3.2 to 5.3.3 by @dependabot in #1910
  • Bump commons-cli:commons-cli from 1.8.0 to 1.9.0 in /src/common/com.smi.microservices.parent by @dependabot in #1914
  • Bump org.apache.maven.plugins:maven-surefire-report-plugin from 3.3.1 to 3.4.0 in /src/common/com.smi.microservices.parent by @dependabot in #1913
  • Bump ch.qos.logback:logback-classic from 1.5.6 to 1.5.7 in /src/common/com.smi.microservices.parent by @dependabot in #1912
  • Bump org.apache.maven.plugins:maven-surefire-plugin from 3.3.1 to 3.4.0 in /src/common/com.smi.microservices.parent by @dependabot in #1911
  • Fix handling of GlobalOptions deserializing to null by @rkm in #1917
  • Bump NUnit from 4.1.0 to 4.2.0 by @dependabot in #1919
  • Bump Microsoft.NET.Test.Sdk and Microsoft.CodeCoverage by @dependabot in #1920
  • Bump NUnit from 4.2.0 to 4.2.1 by @dependabot in #1921
  • Bump NUnit from 4.2.1 to 4.2.2 by @dependabot in #1923
  • Bump YamlDotNet from 16.0.0 to 16.1.0 by @dependabot in #1924
  • Bump org.apache.maven.plugins:maven-surefire-report-plugin from 3.4.0 to 3.5.0 in /src/common/com.smi.microservices.parent by @dependabot in #1925
  • Bump org.apache.maven.plugins:maven-surefire-plugin from 3.4.0 to 3.5.0 in /src/common/com.smi.microservices.parent by @dependabot in #1926
  • Bump org.mockito:mockito-core from 5.12.0 to 5.13.0 in /src/common/com.smi.microservices.parent by @dependabot in #1927
  • Bump StackExchange.Redis from 2.8.0 to 2.8.12 by @dependabot in #1930
  • Bump Moq from 4.20.70 to 4.20.71 by @dependabot in #1929
  • Bump Microsoft.CodeCoverage from 17.11.0 to 17.11.1 by @dependabot in #1928
  • Bump ch.qos.logback:logback-classic from 1.5.7 to 1.5.8 in /src/common/com.smi.microservices.parent by @dependabot in #1933
  • Bump Moq from 4.20.71 to 4.20.72 by @dependabot in #1932
  • Bump Microsoft.NET.Test.Sdk from 17.11.0 to 17.11.1 by @dependabot in #1931
  • Bump NLog from 5.3.3 to 5.3.4 by @dependabot in #1935
  • Bump StackExchange.Redis from 2.8.12 to 2.8.16 by @dependabot in #1934
  • Bump actions/setup-java from 4.2.2 to 4.3.0 by @dependabot in #1936
  • Bump YamlDotNet from 16.1.0 to 16.1.2 by @dependabot in #1937
  • allow specifying path to DynamicRules file by @rkm in #1938
  • bump sqlserver to 2022 in CI to fix startup crash by @rkm in #1940
  • Fix loading TesseractEngine on Linux by @rkm in #1939
  • Release v5.8.0 by @rkm in #1941

Full Changelog: v5.7.2...v5.8.0

Contributors

jas88, rkm, and dependabot
Assets 7
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v5.7.2

29 Jul 15:25
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v5.7.2

Feature

  • #1889 by jas88. Make DB exception handling DB-agnostic rather than MySQL specific

Bugfix

  • #1887 by rkm. Pass setInitialDatabase as true to GetDistinctLiveDatabaseServer to ensure that the correct database is used when connecting to Postgres
  • #1888 by rkm. Ensure keyTag is properly wrapped in QuerySyntaxHelper for Postgres support

What's Changed

Full Changelog: v5.7.1...v5.7.2

Contributors

jas88, rkm, and dependabot
Assets 6
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v5.7.1

24 Jul 09:57
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v5.7.1
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v5.7.1

Feature

  • #1876 by rkm. Manually bump DicomTypeTranslation, IsIdentifiable, YamlDotNet, and RDMP libs

What's Changed

  • Bump HIC.RDMP.Plugin.Test from 8.1.6 to 8.1.7 by @dependabot in #1861
  • Bump StackExchange.Redis from 2.7.33 to 2.8.0 by @dependabot in #1860
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.17.1 to 2.17.2 in /src/common/com.smi.microservices.parent by @dependabot in #1862
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.17.1 to 2.17.2 in /src/common/com.smi.microservices.parent by @dependabot in #1863
  • Bump Terminal.Gui from 1.17.0 to 1.17.1 by @dependabot in #1872
  • Bump System.IO.Abstractions.TestingHelpers from 21.0.22 to 21.0.26 by @dependabot in #1871
  • Bump System.IO.Abstractions from 21.0.22 to 21.0.26 by @dependabot in #1867
  • Bump org.apache.maven.plugins:maven-surefire-report-plugin from 3.3.0 to 3.3.1 in /src/common/com.smi.microservices.parent by @dependabot in #1866
  • Bump org.apache.maven.plugins:maven-surefire-plugin from 3.3.0 to 3.3.1 in /src/common/com.smi.microservices.parent by @dependabot in #1865
  • Bump actions/setup-dotnet from 4.0.0 to 4.0.1 by @dependabot in #1864
  • Bump HIC.RDMP.Plugin from 8.1.7 to 8.2.0 by @dependabot in #1869
  • Bump HIC.FAnsiSql from 3.2.5 to 3.2.6 by @dependabot in #1873
  • Bump DicomTypeTranslation, IsIdentifiable, YamlDotNet, and RDMP libs by @rkm in #1876
  • Release v5.7.1 by @rkm in #1877

Full Changelog: v5.7.0...v5.7.1

Contributors

rkm and dependabot
Assets 6
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v5.7.0

24 Jun 17:32
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v5.7.0

Feature

  • #1679 by darshad-github. Add dicom-anonymiser (Generic Wrapper Microservice)
  • #1723 by rkm. bump CI image to ubuntu-22.04
  • #1748 by howff. Add support for Dermatology SRs
  • #1823 by rkm. Bump to .NET 8.0 and C# 12
  • #1833 by jas88. Move SecurityCodeScan.VS2019 analysis to run as part of CodeQL CI checks not in IDE
  • #1834 by jas88. Update to NUnit v4 API
  • #1843 by jas88. Update DicomLoader switches and docs
  • #1844 by rkm. Tidy some files in DicomAnonymiser
  • #1845 by darshad-github. Update dicom-anonymiser docs
  • #1848 by rkm. replace archived prettier mirror with mdformat

Bugfix

  • #1840 by jas88. Escape multiline CSV properly via CsvHelper

Doc

  • #1831 by rkm. Refresh all documentation

    • Simplify the top-level README, as this content has been migrated to SMI/docs
    • Move READMEs for all tools inside the top-level docs/ to improve navigation
    • Add script for checking docs
    • Add markdown-link-check hook
    • Delete unused TriggerUpdates MongoDB source

Removal

What's Changed

  • SR handling supports the odd structure inside Dermatology SRs by @howff in #1748
  • Bump ch.qos.logback:logback-classic from 1.5.5 to 1.5.6 in /src/common/com.smi.microservices.parent by @dependabot in #1801
  • Bump commons-cli:commons-cli from 1.6.0 to 1.7.0 in /src/common/com.smi.microservices.parent by @dependabot in #1802
  • delete SRAnonTool files by @rkm in #1804
  • Bump Spectre.Console from 0.48.0 to 0.49.0 by @dependabot in #1805
  • Bump NLog from 5.2.8 to 5.3.1 by @dependabot in #1810
  • Bump LibArchive.Net from 0.1.4 to 0.1.5 by @dependabot in #1809
  • Bump Spectre.Console from 0.49.0 to 0.49.1 by @dependabot in #1807
  • Bump NLog from 5.3.1 to 5.3.2 by @dependabot in #1815
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.17.0 to 2.17.1 in /src/common/com.smi.microservices.parent by @dependabot in #1814
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.17.0 to 2.17.1 in /src/common/com.smi.microservices.parent by @dependabot in #1813
  • Bump codecov/codecov-action from 4.3.0 to 4.3.1 by @dependabot in #1812
  • Bump YamlDotNet from 15.1.2 to 15.1.4 by @dependabot in #1817
  • Bump org.mockito:mockito-core from 5.11.0 to 5.12.0 in /src/common/com.smi.microservices.parent by @dependabot in #1818
  • Bump codecov/codecov-action from 4.3.1 to 4.4.0 by @dependabot in #1821
  • Bump com.google.code.gson:gson from 2.10.1 to 2.11.0 in /src/common/com.smi.microservices.parent by @dependabot in #1819
  • .NET 8 by @rkm in #1823
  • Bump Microsoft.NET.Test.Sdk from 17.9.0 to 17.10.0 by @dependabot in #1827
  • Bump codecov/codecov-action from 4.4.0 to 4.4.1 by @dependabot in #1829
  • Bump commons-cli:commons-cli from 1.7.0 to 1.8.0 in /src/common/com.smi.microservices.parent by @dependabot in #1830
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1832
  • Move SecurityCodeScan from IDE integration to CI run as for RDMP by @jas88 in #1833
  • Feature/nunit api by @jas88 in #1834
  • Bump Terminal.Gui from 1.16.0 to 1.17.0 by @dependabot in #1838
  • Bump YamlDotNet from 15.1.4 to 15.1.6 by @dependabot in #1839
  • Bump HIC.RDMP.Plugin.Test, HIC.RDMP.Plugin, HIC.FAnsiSql, CsvHelper and NUnit by @dependabot in #1835
  • Bugfix/csv by @jas88 in #1840
  • Update README and docs by @rkm in #1831
  • Bump HIC.FAnsiSql from 3.2.3 to 3.2.5 by @dependabot in #1841
  • dicom-anonymiser Generic Wrapper Microservice by @darshad-github in #1679
  • Feature/dicomloaderflags by @jas88 in #1843
  • Dicom Anonymiser tidy files by @rkm in #1844
  • dicom-anonymiser Generic Wrapper Microservice Updates by @darshad-github in #1845
  • replace prettier with mdformat by @rkm in #1848
  • Bump CI runner image to ubuntu-22.04 by @rkm in #1723
  • Bump org.apache.commons:commons-configuration2 from 2.10.1 to 2.11.0 in /src/common/com.smi.microservices.parent by @dependabot in #1849
  • Bump codecov/codecov-action from 4.4.1 to 4.5.0 by @dependabot in #1854
  • Bump YamlDotNet from 15.1.6 to 15.3.0 by @dependabot in #1853
  • Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.9.2 to 4.10.0 by @dependabot in #1852
  • Bump org.apache.maven.plugins:maven-surefire-report-plugin from 3.2.5 to 3.3.0 in /src/common/com.smi.microservices.parent by @dependabot in #1851
  • Bump org.apache.maven.plugins:maven-surefire-plugin from 3.2.5 to 3.3.0 in /src/common/com.smi.microservices.parent by @dependabot in #1850
  • Bump CsvHelper from 32.0.3 to 33.0.1 by @dependabot in #1858
  • Bump HIC.RDMP.Plugin from 8.1.6 to 8.1.7 by @dependabot in #1857
  • Bump System.IO.Abstractions.TestingHelpers from 21.0.2 to 21.0.22 by @dependabot in #1856
  • Bump System.IO.Abstractions from 21.0.2 to 21.0.22 by @dependabot in #1855
  • Release v5.7.0 by @rkm in #1859

Full Changelog: v5.6.1...v5.7.0

Contributors

jas88, howff, and 4 other contributors
Assets 6
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v5.6.1

19 Apr 16:15
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v5.6.1
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v5.6.1

Bugfix

  • #1799 by rkm. Re-add a parameterless constructor to DynamicRejector so it can be loaded via reflection in CohortExtractorHost.

What's Changed

  • fix DynamicRejector constructor to allow reflection by @rkm in #1799
  • Release v5.6.1 by @rkm in #1800

Full Changelog: v5.6.0...v5.6.1

Contributors

rkm
Assets 7
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v5.6.0

16 Apr 13:12
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v5.6.0

Feature

  • #1735 by rkm. Add support for CohortPackager to process ExtractedFileVerificationMessages in batches
    • Enabled with CohortPackagerOptions.VerificationMessageQueueProcessBatches
    • Process rate configured with CohortPackagerOptions.VerificationMessageQueueFlushTimeSeconds. Defaults to 5 seconds if not set
  • #1746 by rkm. Start to refactor RabbitMqAdapter logic into generic interface
    • Rename IRabbitMqAdapter -> IMessageBroker
    • Move into Smi.Common.Messaging namespace
    • Add MessageBrokerType and MessageBrokerFactory
    • Create ConnectionFactory directly in RabbitMQBroker
    • Tidy unused variables and naming
  • #1749 by rkm. Refactor and simplify extraction reports
    • Generate a single FailureStoreReport which can be further processed depending on the need
    • Removed ReportFormat and ReporterType from CohortPackagerOptions
    • Merge JobReporterBase and FileReporter into JobReporter

Bugfix

  • #1703 by jas88. Update to fix issues in installation script in docs

Change

  • #1729 by rkm. Rename branch references from master to main

Removal

  • #1730 by rkm. Disable services from Windows CI
  • #1747 by rkm. Remove unused JetBrains.Annotations package

What's Changed

  • Disable services from windows CI by @rkm in #1730
  • rename references from master to main by @rkm in #1729
  • Bump IsIdentifiable from 0.2.1 to 0.3.0 by @dependabot in #1731
  • Bump StackExchange.Redis from 2.7.10 to 2.7.17 by @dependabot in #1733
  • Bump org.mockito:mockito-core from 5.9.0 to 5.10.0 in /src/common/com.smi.microservices.parent by @dependabot in #1742
  • Bump codecov/codecov-action from 3.1.4 to 3.1.5 by @dependabot in #1741
  • Bump System.IO.Abstractions.TestingHelpers from 20.0.4 to 20.0.15 by @dependabot in #1740
  • Bump YamlDotNet from 13.7.1 to 15.1.0 by @dependabot in #1738
  • Bump System.IO.Abstractions from 20.0.4 to 20.0.15 by @dependabot in #1737
  • Bump Terminal.Gui from 1.14.1 to 1.15.1 by @dependabot in #1736
  • Feature/cohort packager status batches by @rkm in #1735
  • Bump YamlDotNet from 15.1.0 to 15.1.1 by @dependabot in #1743
  • Bump codecov/codecov-action from 3.1.5 to 4.0.1 by @dependabot in #1744
  • remove JetBrains.Annotations package by @rkm in #1747
  • Start to abstract message brokers by @rkm in #1746
  • Bump Microsoft.NET.Test.Sdk from 17.8.0 to 17.9.0 by @dependabot in #1752
  • Bump HIC.RDMP.Dicom from 7.0.1 to 7.0.2 by @dependabot in #1760
  • Bump ch.qos.logback:logback-classic from 1.4.14 to 1.5.0 in /src/common/com.smi.microservices.parent by @dependabot in #1758
  • Bump NunitXml.TestLogger from 3.1.15 to 3.1.20 by @dependabot in #1764
  • Bump codecov/codecov-action from 4.0.1 to 4.0.2 by @dependabot in #1761
  • Bump StackExchange.Redis from 2.7.17 to 2.7.20 by @dependabot in #1762
  • Bump Microsoft.CodeAnalysis.CSharp.Scripting from 4.8.0 to 4.9.2 by @dependabot in #1771
  • Bump StackExchange.Redis from 2.7.20 to 2.7.27 by @dependabot in #1770
  • Bump YamlDotNet from 15.1.1 to 15.1.2 by @dependabot in #1769
  • Bump org.mockito:mockito-core from 5.10.0 to 5.11.0 in /src/common/com.smi.microservices.parent by @dependabot in #1768
  • Bump ch.qos.logback:logback-classic from 1.5.0 to 1.5.2 in /src/common/com.smi.microservices.parent by @dependabot in #1767
  • Bump codecov/codecov-action from 4.0.2 to 4.1.0 by @dependabot in #1766
  • Bump actions/setup-java from 4.0.0 to 4.1.0 by @dependabot in #1765
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.16.1 to 2.16.2 in /src/common/com.smi.microservices.parent by @dependabot in #1777
  • Bump org.apache.maven.plugins:maven-assembly-plugin from 3.6.0 to 3.7.0 in /src/common/com.smi.microservices.parent by @dependabot in #1776
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.16.1 to 2.16.2 in /src/common/com.smi.microservices.parent by @dependabot in #1774
  • Bump ch.qos.logback:logback-classic from 1.5.2 to 1.5.3 in /src/common/com.smi.microservices.parent by @dependabot in #1775
  • Bump softprops/action-gh-release from 1 to 2 by @dependabot in #1773
  • Refactor & simplify extraction reports by @rkm in #1749
  • Bump org.apache.commons:commons-configuration2 from 2.9.0 to 2.10.1 in /src/common/com.smi.microservices.parent by @dependabot in #1784
  • Bump actions/setup-java from 4.1.0 to 4.2.1 by @dependabot in #1783
  • Bump com.fasterxml.jackson.dataformat:jackson-dataformat-yaml from 2.16.2 to 2.17.0 in /src/common/com.smi.microservices.parent by @dependabot in #1781
  • Bump com.fasterxml.jackson.core:jackson-databind from 2.16.2 to 2.17.0 in /src/common/com.smi.microservices.parent by @dependabot in #1780
  • Bump org.apache.maven.plugins:maven-assembly-plugin from 3.7.0 to 3.7.1 in /src/common/com.smi.microservices.parent by @dependabot in #1785
  • Bump Terminal.Gui from 1.15.1 to 1.16.0 by @dependabot in #1790
  • Bump codecov/codecov-action from 4.1.0 to 4.1.1 by @dependabot in #1789
  • Bump StackExchange.Redis from 2.7.27 to 2.7.33 by @dependabot in #1788
  • Bump System.IO.Abstractions.TestingHelpers from 20.0.15 to 21.0.2 by @dependabot in #1787
  • Bump System.IO.Abstractions from 20.0.15 to 21.0.2 by @dependabot in #1786
  • Fix install script issues from JIRA RDMP-78 by @jas88 in #1703
  • Bump codecov/codecov-action from 4.1.1 to 4.2.0 by @dependabot in #1791
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #1793
  • Bump codecov/codecov-action from 4.2.0 to 4.3.0 by @dependabot in #1797
  • Bump com.rabbitmq:amqp-client from 5.20.0 to 5.21.0 in /src/common/com.smi.microservices.parent by @dependabot in #1796
  • Bump ch.qos.logback:logback-classic from 1.5.3 to 1.5.5 in /src/common/com.smi.microservices.parent by @dependabot in #1795
  • Bump coverlet.msbuild from 6.0.0 to 6.0.2 by @dependabot in #1794
  • Prepare 5.6.0 release by @rkm in #1798

Full Changelog: v5.5.0...v5.6.0

Contributors

jas88, rkm, and 2 other contributors
Assets 7
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v5.5.0

18 Jan 19:43
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v5.5.0

Feature

  • #1583 by rkm. Add DynamicRulesTester application
  • #1599 by rkm. Enable the C# nullable feature and fix all warnings.
  • #1619 by rkm. Add Modality to ExtractFileMessage classes
  • #1622 by rkm. Add LossyImageCompressionMethod to CTP allowlist
  • #1637 by rkm. upgrade to NET7 and C# 11
  • #1663 by karacolada. Add field UserName to ExtractionRequestInfoMessage
  • #1701 by rkm. Adds the ability for consumers to optionally "hold" unprocessable messages so they are not returned to the queue.

Bugfix

  • #1524 by howff. StructuredReport improvements - collect names from anywhere in text body not just in header
  • #1562 by howff. DicomText - Redact all tags which have a data type (VR) of 'DT' (DateTime). It was already doing dates and names.
  • #1611 by howff. CTP_SRAnonTool - implement a full HTML parser (with other sanity checks) for HTML in TextValue in SRs
  • #1639 by rkm. catch any exception raised during file classification. Fixes #1638
  • #1671 by rkm. disable debug logging spam from external CTP libraries
  • #1684 by jas88. Fix SQL in documentation area - missing semicolons causing syntax error
  • #1704 by rkm. Improve quality of log output
  • #1717 by rkm. update CI release script for upload-artifact@v4

Docs

  • #1572 by jas88. Document installation steps for new users

Removal

Update

  • #1664 by jas88. Update RDMP API to reduce casting

What's Changed

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Contributors

jas88, howff, and 4 other contributors
Assets 7
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v5.4.0

25 Apr 13:12
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v5.4.0
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v5.4.0

Feature

  • #1489 by howff. CTP_DicomToText has options to control the output formatting (especially redaction of HTML and replacement of newlines)

Bugfix

  • #1379 by rkm. Constrain protobuf version to "<3.20.0", since this is the last version which supports python3.6 and we only have 3.6 on the live system.
  • #1396 by jas88. Fix some issues encountered loading DICOM to Mongo in HIC deployment
  • #1399 by jas88. Revert to [email protected] due to disappearance of 3.7.0
  • #1430 by rkm. Add RabbitMQ management port to docker-compose files
  • #1431 by rkm. restrict mysql_connector_python version for python 3.6
  • #1448 by rkm. Add 0.1% threshold for Codecov to report CI failure
  • #1492 by rkm. add codecov token to CI
  • #1493 by rkm. ignore BasicRules.yaml in pre-commit codespell config
  • #1497 by rkm. Fix MongoDB Windows CI by changing to sc.exe
  • #1506 by darshad-github. Fix issue with hidden directories in extraction output paths generated by cohort extractor.
  • #1509 by jas88. Change Windows service control operation timeout to 300s since Mongo sometimes takes longer than the default 30s causing timeout errors otherwise

Doc

  • #1499 by karacolada. update CTP build docs

Meta

  • #1401 by rkm. Condense formatting options into .editorconfig and add more hooks
  • #1407 by rkm. Bump SDK to 6.0.403
  • #1428 by rkm. Add development support for ARM / M1 Mac
  • #1442 by rkm. Switch coverage to Codecov
  • #1450 by darshad-github. Update contributing.md with feature branch workflow guidelines
  • #1451 by rkm. adopt dotnet central package management (CPM)
  • #1468 by rkm. switch rabbitmq docker-compose images to include management plugin
  • #1494 by rkm. [actions] replace deprecated set-output with GITHUB_OUTPUT
  • #1496 by rkm. add CodeQL scan

What's Changed

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Contributors

jas88, howff, and 5 other contributors
Assets 7
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v5.3.0

08 Nov 20:24
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v5.3.0
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v5.3.0

Feature

  • #1259 by rkm. Add support for extraction processing failures
    • Remove IsIdentifiable field from ExtractedFileVerificationMessage and replace with new VerifiedFileStatus enum
    • Update extraction job classes in CohortPackager to store this new field, and handle backwards-incompatibility when reading older extraction logs

Bugfix

  • #1285 by howff. Improve the removal of HTML tags from StructuredReport (SR) text
  • #1314 by jas88. Replace SharpCompress usage due to buggy LZMA handling to fix issue #1313
  • #1350 by tznind. Fix DicomRelationalMapper when running with a YamlRepository backend

Change

  • #1270 by tznind. Rename yaml config file IsIdentifiableBaseOptions to IsIdentifiableOptions and removed unused CLI verbs in smi

Meta

  • #1261 by jas88. Update caching strategy in CI

What's Changed

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Contributors

jas88, howff, and 5 other contributors
Assets 7
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